I think it's fine. I'm a Christian attending a graduate theology school and it wouldn't bother me if an atheist used a biblical name. I would probably assume someone who used a more obscure biblical name is Christian/Jewish, however. I find that such names are most often used by conservative evangelical Christian or (in the case of Hebrew names) Jewish families.

If you like a name, go for it. The Bible is a foundational piece of Western literary/cultural heritage and has significance even if you aren't religious.

I really think it depends on how closely they're associated as well as if there are other well known namesakes.

So a name like Abraham, while it's very associated with Judaism, is also held by some very famous namesakes. So if I met someone named Abe, I'd be just as likely to assume their parents admired AbrahamLincoln as to assume they were deeply religious.

I'm not really sure where the line is, but I certainly wouldn't be offended in any way, except maybe if someone used Judas. Like others have said, it's more an issue of assuming you're religious because of Malachi or Zachariah. But names like Esther, Ruth, Lydia, Felix, and others....weren't even originally part of Judaism or Christianity--they were from other nations, so just because they happen to be in the Bible doesn't mean they're unusable.

I wouldn't be offended, but like others said I would probably assume that you were religious. If I knew that you weren't religious, I would probably think it was a little odd, but if that doesn't bother you then go for it.